Nuclear bodies (NBs) are subnuclear mega-protein or -protein/RNA complexes in both animal and plant cells providing microenvironments for the regulation of gene expression, DNA replication, and DNA repair. An accumulating body of evidence from the studies on animal transcription factories, PML bodies, Cajal bodies, and polycomb bodies suggests that some NBs are transcriptional regulatory hubs directly associated with target genes. However, the basic principles of the interaction between nuclear bodies and chromatin, including molecular mechanisms of how chromatin loci are recruited to nuclear bodies and how nuclear bodies control transcription, remain enigmatic. The long- term goal of our laboratory is to use phytochrome NBs in Arabidopsis as a genetic model to investigate general principles of NB function in eukaryotic cell signaling. Phytochromes are red and far-red photoreceptors mediating light-dependent plant development through transcriptional regulation. Photo-activation and -deactivation of phytochromes triggers rapid NB assembly and disassembly and dramatic reprogramming of the transcriptome. However, the relationship between phytochrome NBs and gene regulation is completely unknown. Our preliminary studies demonstrated that phytochrome NBs are directly associated with phytochrome-repressed genes. Therefore, we hypothesize that phytochrome NBs are central hubs for light-mediated gene silencing. To further test this hypothesis, we propose to identify global phytochrome NB associated chromosome loci using chromatin- precipitation followed by deep sequencing (ChIP-seq), to determine the relationship between gene positioning to phytochrome NBs and transcriptional activity, and to identify cis-elements required for recruiting gene loci to phytochrome NBs. These experiments will provide direct evidence for the function of phytochrome NBs in gene expression and begin to uncover mechanisms involved in recruiting genes to phytochrome NBs. A better understanding of the function of phytochrome NBs will not only uncover novel mechanisms of light signaling in plants, but also provide great insight into evolutionarily conserved mechanisms of nuclear organization and transcriptional regulation.